Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_035239686.1 Q366_RS12820 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000745975.1:WP_035239686.1 Length = 461 Score = 266 bits (681), Expect = 8e-76 Identities = 160/443 (36%), Positives = 246/443 (55%), Gaps = 16/443 (3%) Query: 8 KELPGPKAKEVIERNFKYLAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVIN 67 + +PGPK+ + + ++ +M + P+V ++G G V D DGN++ D +GV V + Sbjct: 20 ESVPGPKSLKQLGEAPEFESMA-RGAGRFPVVYDQGFGATVKDPDGNLYIDITAGVAVNS 78 Query: 68 VGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPGDIERKVV--YGNSGA 125 VG HPRVVEAI KQ K H S D + LA+K+ + P ++ + + SG+ Sbjct: 79 VGRLHPRVVEAIHKQTGKLMHGS--DCSSSMRLDLAKKISGIMPAGLKDNCITFFTQSGS 136 Query: 126 EANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYP 185 A E+A+K V+ TGR Q +AF+ A+HG SLT ++D F P +PGV H+PYP Sbjct: 137 SALESAIKFVRKITGRSQIVAFHGAYHGVHCGCGSLTTGDQYRKD-FGPFIPGVVHVPYP 195 Query: 186 NPYRNTWGIDGYEEPDELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGF 245 YR +G E +++ L+++ + V ++GA+ E QGEGGY+ P F Sbjct: 196 YAYRCCFGTKSQEACEDMCANYLEYLLNTPYTGVD--DVGAVIIEAQQGEGGYLAPNPEF 253 Query: 246 FKALKKFADEYGILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIH 305 + +K +++G L DEVQ G GR+GK WAIEH GVEPD++ FGK IGG +P+AGV Sbjct: 254 LQRVKASCEKHGALFIADEVQSGAGRSGKMWAIEHSGVEPDILTFGKGIGGDVPMAGVTL 313 Query: 306 RADITFD-KPGRHATTFGGNPVAIAAGIEVVEIVKE----LLPHVQEVGDYLHKYLEEFK 360 R D+ + G TF N V+ A + ++I+ E L+ V ++G+ + L+E Sbjct: 314 RKDLAAKIEDGSQPNTFAANGVSAAVSMTNIDILTENDNALIKRVAKLGEQIKDRLKEGA 373 Query: 361 EKYEVIGDARGLGLAQAVEIVKSKETKEKY-PELRDRIVKESAKRGLVLLGCG--DNSIR 417 E IGD RG G +E+VK +ETK + L +++ +G++L+ CG N IR Sbjct: 374 RNIECIGDVRGRGFMIGIELVKDRETKAPFDAALMGQVIMAMLNKGVILVPCGRYGNVIR 433 Query: 418 FIPPLIVTKEEIDVAMEIFEEAL 440 F+P L K+ +D A +I + L Sbjct: 434 FMPSLTTPKKYLDKASDILLDVL 456 Lambda K H 0.320 0.141 0.418 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 556 Number of extensions: 32 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 445 Length of database: 461 Length adjustment: 33 Effective length of query: 412 Effective length of database: 428 Effective search space: 176336 Effective search space used: 176336 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory